This paper describes the use of cyclodextrins (CDs) to improve the determination of fluoroquinolone antibiotics in human body fluids using surface-enhanced Raman spectroscopy (SERS). CDs were used to (i) prepare the CD-SERS substrate (synthesis and stabilization of silver nanoparticles), (ii) increase the sensitivity of the assay by enhancing the interaction between analyte molecules and the substrate, and (iii) improve the analysis accuracy by reducing the interaction between the substrate and endogenous components of body fluids. Two native CDs (α-CD and ß-CD) and two of their derivatives with hydroxypropyl groups were tested, and the best results were obtained with CD-SERS substrate prepared using native ß-CD. The CD-SERS assay has been developed and optimized for the determination of commonly used and structurally related fluoroquinolones (ciprofloxacin, norfloxacin, pefloxacin, and levofloxacin) in urine and blood plasma samples. Importantly, the non-significant difference in the interaction of the CD-modified SERS substrate with various fluoroquinolones has been successfully used to develop a versatile assay suitable for the analyte-class-specific analysis. Calibration plots were obtained for concentration ranges suitable for the determination of the antibiotics in urine (50-500 µg mL-1) and blood plasma (1-6 µg mL-1). The following figures of merit were obtained (for urine and blood plasma, respectively): RSD values are ≤15% and ≤23%, LOD values are 2.9-5.8 and 0.05-0.34 µg mL-1, recovery ranges are 96-105% and 91-111%. In addition, the influence of excessive concentrations of some main endogenous components of the body fluids on the analytical signal was studied. This step was used to evaluate possible limitations of the assay associated with the deviation of the composition of the body fluid matrix. Therefore, accounting for the short analysis time (≤15 min) and the use of a portable Raman spectrometer, the proposed assay can be suggested for therapeutic drug monitoring in hospitals.